Identifying Genetic Dependencies in Cancer by Analyzing siRNA Screens in Tumor Cell Line Panels.
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Date
2018-01-01Author
Campbell, J
Ryan, CJ
Lord, CJ
Type
Journal Article
Metadata
Show full item recordAbstract
Loss-of-function screening using RNA interference or CRISPR approaches can be used to identify genes that specific tumor cell lines depend upon for survival. By integrating the results from screens in multiple cell lines with molecular profiling data, it is possible to associate the dependence upon specific genes with particular molecular features (e.g., the mutation of a cancer driver gene, or transcriptional or proteomic signature). Here, using a panel of kinome-wide siRNA screens in osteosarcoma cell lines as an example, we describe a computational protocol for analyzing loss-of-function screens to identify genetic dependencies associated with particular molecular features. We describe the steps required to process the siRNA screen data, integrate the results with genotypic information to identify genetic dependencies, and finally the integration of protein-protein interaction data to interpret these dependencies.
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Subject
Cell Line, Tumor
Humans
Osteosarcoma
Bone Neoplasms
Protein Kinases
RNA, Small Interfering
Genomics
RNA Interference
Genotype
Gene Dosage
Mutation
Software
Transcriptome
Protein Interaction Maps
Research team
Gene Function
Language
eng
Date accepted
2017-12-19
License start date
2018-01
Citation
Methods in molecular biology (Clifton, N.J.), 2018, 1711 pp. 83 - 99
Publisher
HUMANA PRESS INC